Coverage for /usr/local/lib/python3.11/dist-packages/pyrocko/gui/sparrow/elements/catalog.py: 53%
258 statements
« prev ^ index » next coverage.py v6.5.0, created at 2023-10-06 15:01 +0000
1# https://pyrocko.org - GPLv3
2#
3# The Pyrocko Developers, 21st Century
4# ---|P------/S----------~Lg----------
6# import copy
7import logging
8import operator
9import calendar
10import numpy as num
12from pyrocko.guts import \
13 Object, StringChoice, String, List, Float
15from pyrocko import table, model # , automap
16from pyrocko.client import fdsn, catalog
17from pyrocko.gui.qt_compat import qw
18from pyrocko.plot import beachball
19# from pyrocko.himesh import HiMesh
21# from pyrocko.gui.vtk_util import TrimeshPipe
23from .. import common
25from .table import TableElement, TableState
27logger = logging.getLogger('pyrocko.gui.sparrow.elements.catalog')
29guts_prefix = 'sparrow'
32attribute_names = [
33 'time', 'lat', 'lon', 'northing', 'easting', 'depth', 'magnitude']
35attribute_dtypes = [
36 'f16', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8']
38name_to_icol = dict(
39 (name, icol) for (icol, name) in enumerate(attribute_names))
41# event_dtype = num.dtype(list(zip(attribute_names, attribute_dtypes)))
43t_time = num.float64
46def binned_statistic(values, ibins, function):
47 order = num.argsort(ibins)
48 values_sorted = values[order]
49 ibins_sorted = ibins[order]
50 parts = num.concatenate((
51 [0],
52 num.where(num.diff(ibins_sorted) != 0)[0] + 1,
53 [ibins.size]))
55 results = []
56 ibins_result = []
57 for ilow, ihigh in zip(parts[:-1], parts[1:]):
58 values_part = values_sorted[ilow:ihigh]
59 results.append(function(values_part))
60 ibins_result.append(ibins_sorted[ilow])
62 return num.array(ibins_result, dtype=num.int64), num.array(results)
65def load_text(
66 filepath,
67 column_names=('time', 'lat', 'lon', 'depth', 'magnitude'),
68 time_format='seconds'):
70 with open(filepath, 'r') as f:
71 if column_names == 'from_header':
72 line = f.readline()
73 column_names = line.split()
75 name_to_icol_in = dict(
76 (name, icol) for (icol, name) in enumerate(column_names)
77 if name in attribute_names)
79 data_in = num.loadtxt(filepath, skiprows=1)
81 nevents = data_in.shape[0]
82 c5 = num.zeros((nevents, 5))
83 c5[:, 0] = data_in[:, name_to_icol_in['lat']]
84 c5[:, 1] = data_in[:, name_to_icol_in['lon']]
85 c5[:, 2] = 0.0
86 c5[:, 3] = 0.0
87 c5[:, 4] = data_in[:, name_to_icol_in['depth']] * 1000.
89 tab = table.Table()
90 loc_rec = table.LocationRecipe()
91 tab.add_recipe(loc_rec)
93 tab.add_col(loc_rec.c5_header, c5)
94 for k, unit in [
95 ('time', 's'),
96 ('magnitude', None)]:
98 values = data_in[:, name_to_icol_in[k]]
100 if k == 'time' and time_format == 'year':
101 values = decimal_year_to_time(values)
103 tab.add_col(table.Header(k, unit), values)
105 return tab
108def decimal_year_to_time(year):
109 iyear_start = num.floor(year).astype(num.int64)
110 iyear_end = iyear_start + 1
112 iyear_min = num.min(iyear_start)
113 iyear_max = num.max(iyear_end)
115 iyear_to_time = num.zeros(iyear_max - iyear_min + 1, dtype=t_time)
116 for iyear in range(iyear_min, iyear_max+1):
117 iyear_to_time[iyear-iyear_min] = calendar.timegm(
118 (iyear, 1, 1, 0, 0, 0))
120 tyear_start = iyear_to_time[iyear_start - iyear_min]
121 tyear_end = iyear_to_time[iyear_end - iyear_min]
123 t = tyear_start + (year - iyear_start) * (tyear_end - tyear_start)
125 return t
128def oa_to_array(objects, attribute):
129 return num.fromiter(
130 map(operator.attrgetter(attribute), objects),
131 num.float64,
132 len(objects))
135def eventtags_to_array(events, tab):
137 ks = set()
138 event_tags = []
139 for ev in events:
140 tags = ev.tags_as_dict()
141 ks.update(tags.keys())
142 event_tags.append(tags)
144 for k in sorted(ks):
145 column = [tags.get(k, None) for tags in event_tags]
146 if all(isinstance(v, int) for v in column):
147 dtype = int
148 elif all(isinstance(v, float) for v in column):
149 dtype = float
150 else:
151 dtype = num.string_
152 column = [v or '' for v in column]
154 arr = num.array(column, dtype=dtype)
156 tab.add_col(table.Header('tag_%s' % k), arr)
159def eventextras_to_array(events, tab):
160 n_extras = num.array([len(ev.extras) for ev in events])
161 evts_all_extras = num.arange(len(events))[n_extras != 0]
163 if evts_all_extras.shape[0] == 0:
164 return tab
166 ev0 = events[evts_all_extras[0]]
168 if num.unique(n_extras).shape[0] > 1:
169 msg = 'Not all events have equal number of extras.'
170 if num.unique(n_extras).shape[0] == 2 and num.min(n_extras) == 0:
171 logger.warn(msg + ' Zero length lists are filled with NaNs.')
172 else:
173 raise IndexError(
174 msg + ' Several non-zero shapes detected. Please check.')
176 for key, val in ev0.extras.items():
177 dtype = num.string_
178 values = num.array(['' for x in range(n_extras.shape[0])], dtype=dtype)
180 if type(val) is float:
181 dtype, values = num.float64, num.ones_like(n_extras) * num.nan
183 elif type(val) is int:
184 dtype = num.int64
185 values = num.ones_like(n_extras, dtype=num.int64) * num.nan
187 header = 'extra_%s' % key
188 values[evts_all_extras] = num.array([
189 events[iev].extras[key] for iev in evts_all_extras], dtype=dtype)
191 tab.add_col(table.Header(header), values)
194def events_to_table(events):
195 c5 = num.zeros((len(events), 5))
196 m6 = None
198 for i, ev in enumerate(events):
199 c5[i, :] = (
200 ev.lat, ev.lon, ev.north_shift, ev.east_shift, ev.depth)
202 if ev.moment_tensor:
203 if m6 is None:
204 m6 = num.zeros((len(events), 6))
205 m6[:, 0:3] = 1.0
207 m6[i, :] = beachball.deco_part(ev.moment_tensor, 'deviatoric').m6()
209 tab = table.Table()
211 ev_rec = table.EventRecipe()
212 tab.add_recipe(ev_rec)
213 tab.add_col(ev_rec.get_header('c5'), c5)
215 for k in ['time', 'magnitude']:
216 tab.add_col(ev_rec.get_header(k), oa_to_array(events, k))
218 if events:
219 eventtags_to_array(events, tab)
220 eventextras_to_array(events, tab)
222 if m6 is not None:
223 mt_rec = table.MomentTensorRecipe()
224 tab.add_recipe(mt_rec)
225 tab.add_col(mt_rec.m6_header, m6)
227 return tab
230class LoadingChoice(StringChoice):
231 choices = [choice.upper() for choice in [
232 'file',
233 'fdsn']]
236class FDSNSiteChoice(StringChoice):
237 choices = [key.upper() for key in fdsn.g_site_abbr.keys()]
240class CatalogSelection(Object):
241 pass
244class MemoryCatalogSelection(CatalogSelection):
246 def __init__(self, events=None):
247 if events is None:
248 events = []
250 self._events = events
252 def get_table(self):
253 return events_to_table(self._events)
256class FileCatalogSelection(CatalogSelection):
257 paths = List.T(String.T())
259 def get_table(self):
260 from pyrocko.io import quakeml
262 events = []
263 for path in self.paths:
264 fn_ext = path.split('.')[-1].lower()
265 if fn_ext in ['xml', 'qml', 'quakeml']:
266 qml = quakeml.QuakeML.load_xml(filename=path)
267 events.extend(qml.get_pyrocko_events())
269 if fn_ext in ['dat', 'csv']:
270 assert len(self.paths) == 1
271 tab = load_text(
272 path, column_names='from_header', time_format='year')
274 return tab
276 else:
277 events.extend(model.load_events(path))
279 return events_to_table(events)
282g_catalogs = {
283 'Geofon': catalog.Geofon(),
284 'USGS/NEIC US': catalog.USGS('us'),
285 'Global-CMT': catalog.GlobalCMT(),
286 'Saxony (Uni-Leipzig)': catalog.Saxony()
287}
289g_fdsn_has_events = ['ISC', 'SCEDC', 'NCEDC', 'IRIS', 'GEONET']
291g_sites = sorted(g_catalogs.keys())
292g_sites.extend(g_fdsn_has_events)
295class OnlineCatalogSelection(CatalogSelection):
296 site = String.T()
297 tmin = Float.T()
298 tmax = Float.T()
299 magnitude_min = Float.T(optional=True)
301 def get_table(self):
302 logger.info('Getting events from "%s" catalog.' % self.site)
304 cat = g_catalogs.get(self.site, None)
305 try:
306 if cat:
307 kwargs = {}
308 if self.magnitude_min is not None:
309 kwargs['magmin'] = self.magnitude_min
311 events = cat.get_events(
312 time_range=(self.tmin, self.tmax), **kwargs)
314 else:
315 kwargs = {}
316 if self.magnitude_min is not None:
317 kwargs['minmagnitude'] = self.magnitude_min
319 request = fdsn.event(
320 starttime=self.tmin,
321 endtime=self.tmax,
322 site=self.site, **kwargs)
324 from pyrocko.io import quakeml
325 qml = quakeml.QuakeML.load_xml(request)
326 events = qml.get_pyrocko_events()
328 logger.info('Got %i event%s from "%s" catalog.' % (
329 len(events), '' if len(events) == 1 else 's', self.site))
331 except Exception as e:
332 logger.error(
333 'Getting events from "%s" catalog failed: %s' % (
334 self.site, str(e)))
336 events = []
338 return events_to_table(events)
341class CatalogState(TableState):
342 selection = CatalogSelection.T(optional=True)
343 size_parameter = String.T(default='magnitude', optional=True)
344 color_parameter = String.T(default='depth', optional=True)
346 @classmethod
347 def get_name(self):
348 return 'Catalog'
350 def create(self):
351 element = CatalogElement()
352 return element
355class CatalogElement(TableElement):
357 def __init__(self, *args, **kwargs):
358 TableElement.__init__(self, *args, **kwargs)
359 self._selection_view = None
360 # self._himesh = HiMesh(order=6)
362 # cpt_data = [
363 # (0.0, 0.0, 0.0, 0.0),
364 # (1.0, 0.9, 0.9, 0.2)]
365 #
366 # self.cpt_mesh = automap.CPT(
367 # levels=[
368 # automap.CPTLevel(
369 # vmin=a[0],
370 # vmax=b[0],
371 # color_min=[255*x for x in a[1:]],
372 # color_max=[255*x for x in b[1:]])
373 # for (a, b) in zip(cpt_data[:-1], cpt_data[1:])])
375 def get_name(self):
376 return 'Catalog'
378 def get_size_parameter_extra_entries(self):
379 return ['magnitude']
381 def get_color_parameter_extra_entries(self):
382 return ['depth']
384 def bind_state(self, state):
385 TableElement.bind_state(self, state)
386 self.talkie_connect(state, 'selection', self.update)
388 def update(self, *args):
389 state = self._state
390 # ifaces = None
391 if self._selection_view is not state.selection:
392 self.set_table(state.selection.get_table())
393 self._selection_view = state.selection
395 # ifaces = self._himesh.points_to_faces(self._table.get_col('xyz'))
397 TableElement.update(self, *args)
399 # if ifaces is not None:
400 # ifaces_x, sizes = binned_statistic(
401 # ifaces, ifaces, lambda part: part.shape[0])
402 #
403 # vertices = self._himesh.get_vertices()
404 # # vertices *= 0.95
405 # faces = self._himesh.get_faces()
406 #
407 # values = num.zeros(faces.shape[0])
408 # values[ifaces_x] = num.log(1+sizes)
409 #
410 # self._mesh = TrimeshPipe(vertices, faces, values=values)
411 # cpt = copy.deepcopy(self.cpt_mesh)
412 # cpt.scale(num.min(values), num.max(values))
413 # self._mesh.set_cpt(cpt)
414 # self._mesh.set_opacity(0.5)
416 # self._parent.add_actor(self._mesh.actor)
418 def open_file_dialog(self):
419 caption = 'Select one or more files to open'
421 fns, _ = qw.QFileDialog.getOpenFileNames(
422 self._parent, caption, options=common.qfiledialog_options)
424 if fns:
425 self._state.selection = FileCatalogSelection(
426 paths=[str(fn) for fn in fns])
428 def open_catalog_load_dialog(self):
429 dialog = qw.QDialog(self._parent)
430 dialog.setWindowTitle('Get events from online catalog.')
432 layout = qw.QHBoxLayout(dialog)
434 layout.addWidget(qw.QLabel('Site'))
436 cb = qw.QComboBox()
437 for i, s in enumerate(g_sites):
438 cb.insertItem(i, s)
440 layout.addWidget(cb)
442 pb = qw.QPushButton('Cancel')
443 pb.clicked.connect(dialog.reject)
444 layout.addWidget(pb)
446 pb = qw.QPushButton('Ok')
447 pb.clicked.connect(dialog.accept)
448 layout.addWidget(pb)
450 dialog.exec_()
452 site = str(cb.currentText())
454 vstate = self._parent.state
456 if dialog.result() == qw.QDialog.Accepted:
457 self._state.selection = OnlineCatalogSelection(
458 site=site,
459 tmin=vstate.tmin,
460 tmax=vstate.tmax)
462 def _get_table_widgets_start(self):
463 return 1 # used as y arg in addWidget calls
465 def _get_controls(self):
466 if not self._controls:
467 frame = TableElement._get_controls(self) # sets self._controls
468 layout = frame.layout()
470 lab = qw.QLabel('Load from')
471 pb_file = qw.QPushButton('File')
473 layout.addWidget(lab, 0, 0)
474 layout.addWidget(pb_file, 0, 1)
476 pb_file.clicked.connect(self.open_file_dialog)
478 pb_file = qw.QPushButton('Online Catalog')
480 layout.addWidget(lab, 0, 0)
481 layout.addWidget(pb_file, 0, 2)
483 pb_file.clicked.connect(self.open_catalog_load_dialog)
485 return self._controls
488__all__ = [
489 'CatalogSelection',
490 'FileCatalogSelection',
491 'MemoryCatalogSelection',
492 'CatalogElement',
493 'CatalogState',
494]